[Paraview] MPI performance and VGL error
Dear all, We have compiled paraview server with MPICH2 and parastation , when we deploy the server , it starts with no troubles , the clients connects easily as well . However , when we do some calculations , like a contour, it takes much more time (~3x)to represent the surfaces as when using the client alone Another thing that bothers us, when I start the client with vglrun (through vglconnect ) We get this warning : [VGL] ERROR: Cannot obtain a Pbuffer-enabled 24-bit FB config on the VirtualGL [VGL]server. This is most likely because the 3D X Server :1.2 [VGL]is not configured for 24-bit color or does not have accelerated 3D [VGL]drivers installed. but we have drivers installed and cmake found them . I don't know whether these two problems are related or not , I would like 1) a benchmark or a way to determinate that the server does in fact internal calculations when using mpi 2) How to solve the client issue with VGL our hardware is a Sun x4600 server with 16 CPU cores (8x2 opteron ) with SLES 10 SP2 and four Quadro FX5500 graphics cards. Any help is gladly appreciated, request if you need more information form us Thanks -- Orlando Rivera E-mail: orlando.riv...@lrz.de web:http://www.lrz.de Leibniz-Rechenzentrum Abteilung: Hochleistungssysteme Boltzmannstrasse 1, 85748 Garching Telefon: +49 89 35831-8827 Fax: +49 89 35831-9700 ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
[Paraview] ParaView data
Can I checkout the paraview data from the CVS? There is only a link to the zipped up data on the website. I want to get all the tests running on my system Thanks, Paul ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
[Paraview] Extract cell type from unstructured grid
Hello, Does anyone know an easy way to extract all cells of a particular type from an unstructured grid (without writing code either a plugin or python script)? I was thinking it be possible with the calculator and the number of points in a cell but I can't get access to that. Thanks, Paul ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] ParaView data
Yes you can: cvs -d :pserver:anon...@www.paraview.org:/cvsroot/ParaView3 co ParaViewData On Wed, Feb 18, 2009 at 6:52 AM, Paul Edwards paul.m.edwa...@gmail.com wrote: Can I checkout the paraview data from the CVS? There is only a link to the zipped up data on the website. I want to get all the tests running on my system Thanks, Paul ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] Transformation extraction from Transform filter
Thank you Utkarsh! I used a property iterator to get the names of the properties you suggested; Finally with this lines of code I was able to get the information I needed: vtkSMProxyProperty *Transform_prop = vtkSMProxyProperty::SafeDownCast(myFilters[0]-getProxy()-GetProperty(Transform)); vtkSMProxy* myTransformProxy=Transform_prop-GetProxy(0); vtkSMDoubleVectorProperty *Position_prop = vtkSMDoubleVectorProperty::SafeDownCast(myTransformProxy-GetProperty(Position)); vtkSMDoubleVectorProperty *Rotation_prop = vtkSMDoubleVectorProperty::SafeDownCast(myTransformProxy-GetProperty(Rotation)); Thank you! On Tue, Feb 17, 2009 at 5:23 PM, Utkarsh Ayachit utkarsh.ayac...@kitware.com wrote: The Transform property is a vtkSMProxyProperty. Use GetProxy(0) to get the actual source proxy that produces the transform while is the (extended_sources, Transform3) proxy. It does not have API to access the transform directly, however. You can only get the scale/translation/rotation values. On Tue, Feb 17, 2009 at 4:27 PM, Juan Fernando Duque Lombana jduqu...@eafit.edu.co wrote: Good day everyone, Does anyone knows how to extract the Transform matrix from a Transform filter? I've been trying using the following line: vtkSMDoubleVectorProperty *Transform_prop = vtkSMDoubleVectorProperty::SafeDownCast(myFilterPipeline-getProxy()-GetProperty(Transform)); But when I try to access any: Transform_prop-GetElement(i); I get a segmentation fault, Any hints or ideas? Thank you in advance! ... Juan Fernando Duque Lombana. ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview -- ... Juan Fernando Duque Lombana. ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] Extract cell type from unstructured grid
Paul,
I don't know of any existing filter to do that, but a pretty simple
programmable filter can do it. Here is the script that will achieve it. Just
create a custom filter and copy this into the script.
input = self.GetUnstructuredGridInput() output =
self.GetUnstructuredGridOutput()
output.GetPointData().PassData(input.GetPointData())
output.GetCellData().PassData(input.GetCellData()) cellTypes =
vtk.vtkUnsignedCharArray() cellTypes.DeepCopy(input.GetCellTypesArray())
cellTypes.SetName(Cell Types) output.GetCellData().AddArray(cellTypes)
If you plan to use this multiple times, you probably want to wrap this in a
custom filter.
-Ken
On 2/18/09 5:07 AM, Paul Edwards paul.m.edwa...@gmail.com wrote:
Hello,
Does anyone know an easy way to extract all cells of a particular type from an
unstructured grid (without writing code either a plugin or python script)? I
was thinking it be possible with the calculator and the number of points in a
cell but I can't get access to that.
Thanks,
Paul
Kenneth Moreland
*** Sandia National Laboratories
***
*** *** *** email: kmo...@sandia.gov
** *** ** phone: (505) 844-8919
*** web: http://www.cs.unm.edu/~kmorel
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Re: [Paraview] MPI performance and VGL error
I will have to guess at why, say, contour is running slower. I can think of
two possibilities (but not claiming that either is necessarily correct).
1. Perhaps the data is not distributed. If the reader is naive (you didn't
specify what data you were reading), it could be just loading all of it on node
0. The poor performance could simply be that the data is really being
processed in serial. Run the Process Id Scalars filter on the output of
contour to make sure that the cells are distributed amongst the processes.
2. Some filters (contour included) need ghost cells. When you add them, they
will send a request up the pipeline to load another layer of ghost cells.
Assuming the reader supports it, the reader will usually reload the entire data
set from file on each process to include the ghost cells. There is a good
chance that reading the data from disk is taking a lot longer than contouring
the data. Open the timer log (Tools - Timer Log) and see how much time each
component is taking. If the contour filter is reported to run really fast (or
missing from the timings if faster than the threshold) and the reader is
running multiple times, then that is probably it.
As far as your problems with vglconnect, I am afraid I cannot be much help as I
am unfamiliar with that hardware. (Perhaps someone else on this list has run
into this hardware.) It sounds like the pvserver nodes are having trouble
connecting to the appropriate X displays. Usually this is a matter of getting
your DISPLAY environment variables (or -display command line flags) correct.
-Ken
On 2/18/09 2:31 AM, Orlando Rivera orlando.riv...@lrz.de wrote:
Dear all,
We have compiled paraview server with MPICH2 and parastation , when
we deploy the server , it starts with no troubles , the clients
connects easily as well .
However , when we do some calculations , like a contour, it takes
much more time (~3x)to represent the surfaces as when using the
client alone
Another thing that bothers us, when I start the client with vglrun
(through vglconnect ) We get this warning :
[VGL] ERROR: Cannot obtain a Pbuffer-enabled 24-bit FB config on the
VirtualGL
[VGL]server. This is most likely because the 3D X Server :1.2
[VGL]is not configured for 24-bit color or does not have accelerated 3D
[VGL]drivers installed.
but we have drivers installed and cmake found them .
I don't know whether these two problems are related or not , I would like
1) a benchmark or a way to determinate that the server does in fact
internal calculations when using mpi
2) How to solve the client issue with VGL
our hardware is a Sun x4600 server with 16 CPU cores (8x2 opteron )
with SLES 10 SP2 and four Quadro FX5500 graphics cards.
Any help is gladly appreciated, request if you need more
information form us
Thanks
--
Orlando Rivera
E-mail: orlando.riv...@lrz.de
web:http://www.lrz.de
Leibniz-Rechenzentrum
Abteilung: Hochleistungssysteme
Boltzmannstrasse 1, 85748 Garching
Telefon: +49 89 35831-8827
Fax: +49 89 35831-9700
___
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*** Sandia National Laboratories
***
*** *** *** email: kmo...@sandia.gov
** *** ** phone: (505) 844-8919
*** web: http://www.cs.unm.edu/~kmorel
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[Paraview] Parallel VTK
Hi all, I am trying to use this database (actually, I am attaching just an example) with the ParallelVTK language for Paraview. I get an error message. What's, to you? Thanks for help, Samuele. dati2.vtr Description: XML document dati1.vtr Description: XML document dati.pvtr Description: XML document ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
[Paraview] Parallel VTK
Hi all, I am trying to use this database (actually, I am attaching just an example) with the ParallelVTK language for Paraview. I get an error message. What's, to you? Thanks for help, Samuele. PS: sorry if this is the 2nd email, but I forgot to write [Paraview] in the subject dati2.vtr Description: XML document dati1.vtr Description: XML document dati.pvtr Description: XML document ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
[Paraview] vtkXMLStructuredGridWriter class
Dear all, I am trying to write out a part of my *.vts file into a new *.vts file, where the user can select the i,j,k. In fact I would like to write out the i and k for a given j. In order to do this, I am using the vtkXMLStructuredGridWriter class, in particular the SetWriteExtenthttp://www.vtk.org/doc/release/5.2/html/a01601.html#661ae15ae5c0963599148b55c6041ad0(int, int, int, int, int, int) method. The .vts file contains points data and 9 arrays of data such as velocity etc. If the SetWriteExtent method is called with (1 16 1 11 1 2) for example, every thing works as normal and I can visualize the data using Paraview for example. However, if the argument is (1 1 1 11 1 2), the points are written out, but the arrays containing velocity are not written - well the definitions are written (Float data, etc) - but not the values. What am i doing wrong here? Incidentally I am on VTK-5.2 Perhaps, I am not using the write method, if thats the case can some one please point me towards what method/classes I should be using? Thanks, Rakesh ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
[Paraview] Emissive polygons?
Hello, I'm not sure if I'm using the proper terminology, but is it possible in ParaView to give polygons or 3d cells an emissive property for the lighting, so they give off light instead of reflecting it? Thanks, -Eric -- Eric E Monson Duke Visualization Technology Group ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] Emissive polygons?
I'm afraid not. It looks like that functionality is not even support in VTK.
Implementing light emission that is constant for whole objects would be pretty
straightforward, but would require modifying code all the way to VTK's
rendering layer.
-Ken
On 2/18/09 1:55 PM, Eric E. Monson emon...@cs.duke.edu wrote:
Hello,
I'm not sure if I'm using the proper terminology, but is it possible
in ParaView to give polygons or 3d cells an emissive property for
the lighting, so they give off light instead of reflecting it?
Thanks,
-Eric
--
Eric E Monson
Duke Visualization Technology Group
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Re: [Paraview] xdmf hdf5 gzip compressed data
Hi Johannes, as you're also working with Fortran, I think I can help you a little bit more. I wrapped some files ( http://www.nacad.ufrj.br/~rnelias/paraview/xdmf/xdfm-files.zip) and Fortran routines I use in my program to write the Xdmf as well as the HDF5. It's also a cavity flow dataset (unstructured grid, 5 time steps partitioned in 4 parallel subdomains). Note that the Xdmf files are written using the Fortran's FORMAT statement. I know it's a bit uggly but my data does not vary between runs, so, why would I need to use a library with a bunch of routines if just a couple of Fortran FORMATs solve my problem? Moreover, FORMATs are quite portable between systems without the need to compile or install anything else. By the way, I loaded your files without any problem... Just deleted your system path from the HDF5 DataItem reference, for example: Original: /home/johannes/workspace/XDMF/xdmf_data/LDCF/LDCF.h5:data/coordinates/x_v Modified: LDCF.h5:data/coordinates/x_v Voilá, it works ;o) (thanks God) Of course, the xdmf file, in this case, must be kept in the same directory of the HDF5 files it makes references (I have no idea if Xdmf file could point to HDF5 files in other directories...) I hope it helps you Renato N. Elias == Researcher at High Performance Computing Center (NACAD) Federal University of Rio de Janeiro (UFRJ) - Rio de Janeiro, Brazil http://www.nacad.ufrj.br/~rnelias On Wed, Feb 18, 2009 at 6:49 PM, Johannes Will johannes.w...@tu-harburg.dewrote: Hi Renato, many thanks for your replay, I'd rather have it to do the mistakes myself, and be sure PV is able to process compressed files. Got to sell xdmf to my manager on Friday! We use a fortran based code to produce the hdf5 files, that fore we use the hdf5 APIs. I write the xdmf files with python script on my own, since we did not want to produce yet another dependency. The files I produce work well, if the h5-files are not compressed. I tried to export my case as xdmf from PV3.4 this produces a new h5 and xdmf file. I tried to compress this new file with ' h5repack ', but the resultfile crashes also. I have attached a h5 file we produced. It is the well known Lid Driven Cavity Flow (uncompressed) together with txt-dump and my xdmf file. Maybe you have an idea were I go wrong. Kind regards Johannes Quoting Renato Elias rnel...@gmail.com: Hi Johannes, I use Xdmf/HDF5 in Fortran and my files are compressed. After reading your message I did a test in PV3.4 and the dataset was loaded without any problem. Are you sure that the problem is related to compression? Have you got success in loading uncompressed files? Are you writing your Xdmf files using the library or the files are being made by yourself? Regards Renato. On Tue, Feb 17, 2009 at 6:42 PM, Johannes Will johannes.w...@tu-harburg.dewrote: Hallo everybody, I am working now for quite a while with xdmf, which I find a very good tool. I now tried to process compressed (CHUNK, GZIP) h5 data, and paraview keeps crashing with a 'segmentation fault'. Has anybody some idea about that, or yet tried to process compressed data? Any hint is appreciated. Many Thanks Johannes -- Johannes Will Pulverhofsweg 5 22159 Hamburg Germany Tel.: #49-40-644 199 29 Cell: #49-176-23 600 633 Mail: johannes.w...@tuhh.de ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview -- Johannes Will Pulverhofsweg 5 22159 Hamburg Germany Tel.: #49-40-644 199 29 Cell: #49-176-23 600 633 Mail: johannes.w...@tuhh.de ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
[Paraview] Changing the default volume mapper in Paraview?
Hi everyone. I have debugged paraview for days. The reason is that I want to use vtkOpenGLVolumeTextureMapper3d mapper instead of the default volume mapper vtkFixedPointVolumeRayCastMapper in Paraview. Till now, I haven't figured out how to do that. Has anyone done this before? Any hint and help is greatly appreciated. Thanks, Aaron ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
[Paraview] Parallel VTK
Hi all, I am trying to use this database (actually, I am attaching just an example) with the ParallelVTK language for Paraview. I get an error message. What's, to you? Thanks for help, Samuele. PS: sorry if this is the 2nd email, but I forgot to write [Paraview] in the subject dati2.vtr Description: XML document dati1.vtr Description: XML document dati.pvtr Description: XML document ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] particletracer
Hi John, I downloaded your dataset last night and just got tested it. But I get the exact same error with your dataset as mine! Let me describe exactly what/how I'm doing: 1. Loading the dataset 2. Selecting the dataset and create filter 'temporal cache'. Click Apply. 3. Creating a line from menu 'sources'. Modifying the line where I want to have it. Click Apply. 4. Selecting my dataset go to filters and particletracer. In the new window I'm choosing 'source' as input port. Under 'select source(s)' I'm holding down the shift key and click on temporal cache and line. Then I click OK. 5. Error appears! same as before: ERROR: In ..\..\..\ParaView3\VTK\Filtering\vtkDemandDrivenPipeline.cxx, line 822 vtkCompositeDataPipeline (0D4892A8): Input for connection index 0 on input port index 1 for algorithm vtkTemporalStreamTracer(0D433300) is of type vtkTemporalDataSet, but a vtkDataSet is required. Am I doing something totally wrong?? Cheers, Martin Martin I've put a dataset here ftp://ftp.cscs.ch/out/biddisco/flowviz/damBreakMarin.zip try loading this in paraview, connecting a cache and then a line source. If you are able to generate animated particles then all is well and there is something wrong with your data. If not, then maybe somethig is wrong with paraview cvs and I'd better take a look at it. NB. The dataset supplied is not a very good example as the time variable increments as 0,1,2 etc, and in fact should be much smaller, the particles travel too far each step. I only just remembered after I uploaded it. JB Hi John, the error messages about Multiblock Dataset is showing when I dont use a temporal cache on my input. I tried using just a line source for seed points and I dont get any errors about that. So the problem is: If I just use particletracer on my input and line soure I get error saying Dataset is Multiblock Dataset which is not required. If a use a temporal cache on my input and then make a line source as seed points and connecting the two using the particletracer, it gives error saying dataset is TemporalDataset which is not required. I dont have any idea have to come around this problem. Is there another way to follow 3d flow in a good manner? I've tried streamtracer but dont think you get a clear view. ERROR: In /Users/kitware/Berk/ParaView3/VTK/Filtering/vtkDemandDrivenPipeline.cxx, line 822 vtkCompositeDataPipeline (0x1ff6cd60): Input for connection index 0 on input port index 1 for algorithm vtkTemporalStreamTracer(0x1ff6cdf0) is of type vtkTemporalDataSet, but a vtkDataSet is required. Cheers, Martin Uppman -- Martin Looking at your earlier message it seems like you are setting the seed points using a MultiBlock datastructure. I don't think I've enabled support for multiblock seed points (I will do so after clicking send, but you won't get it for some time). Please try converting your seed points to a simple dataset and retry. The error message saying DataSet is required is on port 1 (seeds) - not port 0 (vector field) - I didn't notice this before. Sorry. Try unsing a line source to start and see if everything works. then move on to more sophisticated stuff. JB Sorry, but this doesnt make any sense to me. I have a 3D dataset with magnitude and velocity (X,Y,Z) for 13 time frames. And as you wrote, paraview internally converts multiple vktDataSets into a TemporalDataSet. But particle tracer requires multiple time steps, why does it then give error that a vktDataSet is required? A vktDataSet, according to what you wrote, is just a single timestep. Martin Martin A single timestep is a vtkDataSet, StremTracer generates streamline through a vector field for this data. The ParticleTracer requires multiple time steps to advect particles through the field over time. The particle tracer requests 2 time steps per iteration from it's input, internally paraview converts multiple vtkDataSets from the input into a TemporalDataSet. JB Thanks you, I can now conenct the two sources. I tried on Windows and found this alternative if I want to use input or source in the particle tracer. When choosing source I could select both dataset and seed source. Problem on my Mac was that the dialog box was to small so I didnt find this option. Btw what is the difference between vtkTemporalDataSet and vktDataSet? ParticleTracer requires vktDataSet which I dont have, is it possible to convert the dataset somehow. I can use filter StreamTracer on my dataset and because StreamTracer and ParticleTracer is based on the same physics, I should be able to visualize particles. ERROR: In /Users/kitware/Berk/ParaView3/VTK/Filtering/vtkDemandDrivenPipeline.cxx, line 822 vtkCompositeDataPipeline (0x225e2020): Input for connection index 0 on input port index 1 for algorithm
